The present invention relates to viologen linked acridine based molecule of the general formula 1 (1a, 1b, 1c, and 1d) 
1a. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-11
R=xe2x80x94MV2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96 or -Pyr2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96; m=1-13
1b. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-11
R=xe2x80x94MV2+xe2x80x94(CH2)m-Acr 2X↓ or -Pyr2+-(CH2)m-Acr 2Xxe2x8ax96; m=1-11
1c. wherein
Y=ortho or para tolyl
R=MV2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96 or -Pyr2xe2x88x92-(CH2)mxe2x80x94CH3 2Xxe2x8ax96; m=1-13
1d. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-10
R=xe2x80x94Acr+-R1 Xxe2x8ax96/2X
wherein
N in the arcridine main ring is also quaternised by alkyl group
R1=xe2x80x94(CH2)mxe2x80x94CH3 and xe2x80x94(CH2)mxe2x80x94C6H4xe2x80x94(CH2)mxe2x80x94CH3 (para), m=0-13,
and wherein 
and/or pharmaceutically acceptable derivative thereof, useful as phototherapeutical and catalytic photoactivated DNA cleaving agents. The present invention also relates to a process for the preparation of the novel molecule of formula 1. The novel molecules of the invention are useful for the stabilization of DNA including duplex, triplex and quadruplex structures through intercalation and/or bisintercalation and groove binding interactions. The novel molecules of the invention are also for the catalytic photoactivated cleavage of DNA purely through cosensitization with selectivity at guanine (G) sites in duplex and AG two base bulge containing sequences.
The present invention also relates to a series of bifunctional molecules of the general formula 1 (1a, 1b, and 1c) and derivatives thereof, are also useful as photocatalysts for the oxidation of water to generate hydrogen in industrial applications.
Design of functional molecules that bind selectively to nucleic acids (DNA or RNA) and are capable of cleaving duplex or single stranded nucleic acids is an active area of research that has important biochemical and biomedical applications. Some of these effective agents have been extremely useful in the treatment of various diseases and also as probes for understanding DNA structures and DNA-protein interactions. While natural restriction enzymes have been very useful in many of these applications, their large size and/or limited range of sequence recognition capabilities prevent their general use. Hence, synthetic functional molecules that cause site-selective or sequence specific modifications of DNA and offer a clean and efficient way of cutting DNA at sites that are not recognized by conventional restriction enzymes are highly required.
In this context, a large number of synthetic ligands have been developed, which have it ability to recognize and bind to specific sequences or structural domains in DNA and exhibit nucleolytic activity under physiological conditions (chemical nucleases) or upon photoactivation (photonucleases). Some of these include, 1,10-phenanthroline-copper, ferrous-EDTA, bleomycin, enediyene antibiotics and anthraquinones. For examples, references may be made to U.S. Pat. No. 5,985,557; No. 6,090,543; No. 5,739,022; No. 5,556,949; No. 5,552,278; No. 5,504,075; No. 4,942,227; Nielsen, P. E. J. Mol. Recog. 1990, 3, 1; Papavassiliou, A. G. Biochem. J. 1995, 305, 345; Sigman, D. S.; Graham, D. R.; D""Aurora, V.; Stern, A. M. J. Biol. Chem. 1979, 254, 12269; Pope, L. E.; Sigman, D. S. Proc. Natl. Acad. Sci. USA. 1984, 81, 3; Tullius, T. D.; Dombroski, B. A. Proc. Natl. Acad. Sci. USA. 1986, 83, 5469; Hertzberg, R. P.; Dervan, P. B. J. Am. Chem. Soc. 1982, 104, 313; Hecht, S. M.; Bleomycin: Chemical, Biochemical and Biological aspects, Ed., Springer Verlag: New York, 1979; Sausville, E. A.; Peisach, J.; Horwitz, S. B. Biochemistty, 1978, 17, 2740. However, synthetic ligands that are versatile and mimic the conventional restriction enzymes are yet to be developed.
Of the several classes of DNA cleaving systems reported, the photoactivated cleaving agents have been found to posses significant practical advantages over the reagents that cleave DNA under thermal conditions. An interesting aspect of the photoactivated DNA cleaving agent is that it allows the reaction to be controlled spatially and temporally by combining all of the components of the reaction mixture before the irradiation. Excitation of the reaction mixture with an appropriate light source initiates the reaction, which continues until the light is shut off The ability to control light, in both spatial and temporal sense would be advantageous for applications ranging from the time resolved probing of various biochemical processes such as transcription and translation to genomic analysis and therapeutic agents. For selected examples, reference may be made to U.S. Pat. No. 5,994,410; No. 5,734,032; No. 5,650,399; No. 5,607,924; No. 6,087,493; No. 6,057,096; 5,767,288: No. 5,439,794; Armitage, B. Chem. Rev. 1998, 98, 1171 and references sited therein; Kochevar, I. E.; Dunn, D. A. Bioorg. Photochem. 1990, 1, 273 and references sited therein; Paillous, N.; Vicendo, P. J. Photochem. Photobiol. B 1993, 20, 203; Nielsen, P. E.; Jeppesen, C.; Buchardt, O. FEBS lett. 1988, 235, 122; Chow, C. S.; Barton, J. K. Methods Enzymol. 1992, 212, 219; Chang, C. -H.; Meares, C. F. Biochemistry 1982, 21, 6332; Riordan, C. G.; Wei, P. J. Am. Chem. Soc. 1994, 116, 2189; Thorp, H. H. Angew. Chem., Int. Ed. Eng. 1991, 30, 1517; Armitage, B.; Yu, C.; Devadoss, C.; Schuster, G. B. J. Am. Chem. Soc. 1994, 116, 9847; Adam, W.; Cadet, J.; Dall""Acqua, F.; Epe, B.; Ramaiah, D.; Saha-Moller, C. R. Angew. Chem. Int. Ed. Engl. 1995, 34, 107; Uesawa, Y.; Kuwahara, J.; Sugiura, Y. Biochem. Biophys. Res. Commun. 1989, 164, 903; Ito, K.; Inoue, S.; Yamamoto, K.; Kawanishi, S. J. Biol. Chem. 1993, 268, 13221; Saito, I.; Takayama, M.; Matsuura, T.; Matsugo, S.; Kawanishi, S. J. Am. Chem. Soc. 1990, 112, 883; Sako, M.; Nagai, K.; Maki, Y. J. Chem. Soc. Chem. Commun. 1993, 750.
These photoactivated cleaving agents found to cleave DNA (i) by generation of diffusible (singlet oxygen) and non-diffusible (hydroxyl radicals) reactive intermediates, (ii) hydrogen atom abstraction and (iii) electron transfer. Most of the systems reported so far, initiate photocleavage by more than one mechanism. Though the damage induced by all these mechanisms lead to the initial modification of either sugar or nucleobase, which then results in phosphodiester cleavage, serious efforts are in progress to develop reagents which cleave DNA purely by one mechanism and also to target these cleaving agents to specific sequences or domains in DNA. References may be made to Cadet, J.; Teoule, R. Photochem. Photobiol. 1978, 28, 661; Croke, D. T.; Perrouault, L.; Sari, M. A.; Battioni, J. P.; Mansuy, D.; Magda, D.; Wright, M. M.; Miller, R. A.; Sessler, J. L.; Sansom, P. L. J. Am. Chem. Soc. 1995, 117, 3629; Theodorakis, E.; Wilcoxen, K. M. Chem. Commun. 1996, 1927; Suenaga, H.; Nakashima, K.; Hamachi, I.; Shinkai, S. Tetrahedron Lett. 1997, 38, 2479; Cullis, P. M.; Malone, M. E.; Merson-Davies, L. A. J. Am. Chem. Soc. 1996, 118, 2775; Sies, H.; Schulz, W. A.; Steenken, S. J. Photochem. Photobiol. B 1996, 32, 97; Saito, I.; Takayama, M.; Sugiyama, H.; Nakamura, T. In DNA and RNA Cleavers and Chemotherapy of Cancer and ViraL Diseases; Meunier, B., Ed.; Kluwer: Netherlands, 1996, pp 163-176.
Recently, there has been growing interest in designing molecules, which cleave DNA effectively through photoinduced electron transfer mechanism involving purely by the oxidation of nucleobases. A unique feature of this mechanism is that one can have reasonable control over the cleavage. It has been observed that DNA cleavage by this mechanism occurs at guanine (G), since guanine is the most easily oxidizable base of the nucleic acids because of its low ionization potential. A large number of organic as well as inorganic systems have been reported which cause DNA cleavage by photoinduced electron transfer mechanism. However, most of these reagents were found to be less efficient with the cleavage efficiency in the order of 10xe2x88x928. References may be made to Sevilla, M. D., D""Arcy, J. B.; Morehouse, K. M.; Englehardt, M. L. Photochem. Pholobiol. 1979, 29, 37; Blau, W.; Croke, D. T.; Kelly, J. M.; McConnel, D. J.; OhUigin, C.; Van der Putten, W. J. M. J. Chem. Soc. Chem. Commun. 1987, 751; Sage, E.; Le Doan, T.; Boyer, V.; Helland, D. E.; Kittler,; Hxc3xa9lxc3xa8ne, C; Moustacchi, E. J. Mol. Biol. 1989, 209, 297; Brun, A. M., Harriman, A. J. Am. Chem. Soc. 1991, 113, 8153; Ly, D.; Kan, Y.; Armitage, B.; Schuster, G. B. J. Am. Chem. Soc. 1996, 118, 8747: Hall, D. B.; Holmlin, R. E.; Barton, J. K. Nature 1996, 382, 731; Gasper, S. M.; Schuster, G. B. J. Am. Chem. Soc. 1997, 119, 12762. Therefore, efficient photoactivated DNA cleaving agents based on electron transfer mechanism are highly desired for biological applications.
In the case of the photoactivated DNA cleaving agents by electron transfer mechanism, the efficiency of the reaction depends on the reduction potential of the cleaving agent, excited state energy and the oxidation potential of the ground state base, in addition to other conditions. For an efficient reaction to occur, the rate of the forward electron transfer from the donor to an acceptor must be greater than the back electron transfer process. Therefore, the inefficiency associated with the photoactivated DNA cleaving agents can be attributed to the existence of an efficient back electron transfer between the resultant oxidized base and the reduced sensitizer. To overcome the drawback of the back electron transfer process associated with such systems, a few examples based on cosensitization mechanism have been developed (Dunn, D. A.; Lin, V. H.; Kochevar, I. E. Biochemistry 1992, 31, 11620; Atherton, S. J.; Beaumont, P. C. J. Phys. Chem. 1987, 91, 3993; Fromherz, P.; Rieger, B. J. Am. Chem. Soc. 1986, 108, 5361). These systems consists of a sensitizer, which is also an intercalator, transfers an electron upon photoactivation to a cosensitizer (electron acceptor), bound on the surface of DNA. The photosensitization involving the cosensitizer that bound far away from the sensitizer is expected to inhibit the back electron transfer and thereby increase the DNA cleavage. However, in reality, only marginal improvement in DNA cleavage efficiency (in the order of 10xe2x88x927) was observed in these systems owing to the complications with respect to the concentration, distance and DNA binding affinities of the sensitizer and cosensitizers.
Therefore, development of small compounds which are, soluble in aqueous medium, overcome the inefficiency due to the back electron transfer, undergo strong binding interactions with DNA, selective and effective in inducing DNA cleavage purely through electron transfer mechanism are highly desired for biological applications including clean and efficient way of cutting DNA at sites that are not recognized by the conventional restriction enzymes.
It is an objective of the present investigation to provide functional molecules which bind strongly and selectively with DNA and act as selective and effective photoactivated DNA cleaving agents which function purely through cosensitization mechanism.
The main objective of the present invention is to provide novel bifunctional molecules based on viologen linked acridines or derivatives thereof, which can be used as phototherapeutical and catalytic photoactivated DNA cleaving agents.
Another objective of the present invention is to provide bifunctional molecules based on viologen linked acridines or derivatives thereof, which can act as probes for various DNA structures (single strand, duplex, triplex and quadruplex) of biological significance and with high selectivity.
Yet another objective of the present invention is to provide bifunctional molecules based on viologen linked acridines or derivatives thereof, which can act as catalytic photoactivated DNA cleaving agents of duplex and base bulges containing DNA, purely through cosensitization mechanism.
Still another objective of the present invention is to provide bifunctional molecules based on viologen linked acridines or derivatives thereof, which can act as photocatalysts for the oxidation of water in industrial applications.
Accordingly the present invention relates to viologen linked acridine based molecule of the general formula 1 (1a, 1b, 1c, and 1d)xe2x80x94below 
1a. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-11
R=xe2x80x94MV2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96 or -Pyr2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96; m=1-13
1b. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-11
R=xe2x80x94MV2+xe2x80x94(CH2)mAcr 2Xxe2x8ax96 or -Pyr2+xe2x80x94(CH2)m-Acr 2Xxe2x8ax96; m=1-11
1c. wherein
Y=ortho or para tolyl
R=xe2x80x94MV2+xe2x80x94(CH2)mxe2x80x94CH3 2Xxe2x8ax96 or -Pyr2+(CH2)mxe2x80x94CH3 2Xxe2x8ax96; m=1-13
1d. wherein
Y=xe2x80x94(CH2)nxe2x80x94; n=1-10
R=-Acr+xe2x80x94R1 Xxe2x8ax96/2X
wherein N in the acridine main ring is also quaternised by alkyl group
R1=xe2x80x94(CH2)mxe2x80x94CH3 and xe2x80x94(CH2)mxe2x80x94C6H4xe2x80x94(CH2)mxe2x80x94CH3 (para), m=0-13,
and wherein 
The present invention also relates to a process for the preparation of the novel bifunctional molecule based on viologen linked acridines, bisacridines and acridinium salts of the general formula 1 (1a, 1b, 1c and 1d) above, said process comprising forming a solution of xcfx89-(acridin-9-yl)-xcex1-bromoalkanes and/or 1-alkyl-4,4xe2x80x2-bipyridinium bromides in dry acetonitrile in the ratio of 1:1, stirring the solution at a temperature in the range of 20-50xc2x0 C. for a time period in the range between 8-24 h to obtain a precipitate, filtering, and washing the precipitate with dry acetonitrile and dichloromethane to remove any unreacted starting materials, purifying the solid so obtained to give obtain compound of formula 1 (1a, 1b, 1c and 1d).
In one embodiment of the invention, the compounds of formula 1 are preferably recrystallized from a mixture (1:4) of methanol and acetonitrile.
Yet another embodiment of the present invention relates to bifunctional molecules of the general formula 1 (1a, 1b, 1c and 1d) and pharmaceutically acceptable derivatives thereof for the photocatalytic cleavage of DNA at G sites of duplex and AG two base bulges containing DNA purely through cosensitization mechanism.
In another embodiment of the invention, bifunctional molecules of the general formula 1 (1a, 1b, 1c and 1d) and pharmaceutically acceptable derivatives thereof are used as DNA targeted diagnostic or phototherapeutic agents.
In another embodiment of the present invention the bifunctional molecules of the invention are used for the stabilization of DNA including duplex, triplex and quadruplex structures through intercalation, bisintercalation and groove binding.
Yet another embodiment of the present invention is the use of the bifunctional molecules of general formula 1 (1a, 1b, 1e and 1d) for the photocatalytic cleavage of DNA with selectivity at G sites of duplex and AG two base bulges and as probes for these structures.
Still another embodiment of the present invention is that the bifunctional molecules and derivatives thereof of the general formula 1 (1a, 1b, and 1c) are used as photocatalysts for the oxidation of water in industrial applications.